public Peptide GetFullPeptide() { var aminoAcids = new List <AminoAcidReference>(); foreach (var approximatedAminoAcid in approximatePeptide.AminoAcids) { var aminoAcid = AminoAcidLibrary.Get(approximatedAminoAcid.Name, approximatedAminoAcid.SequenceNumber); PdbAminoAcidAtomNamer.AssignNames(aminoAcid); var nitrogen = aminoAcid.GetAtomFromName("N"); nitrogen.Position = approximatedAminoAcid.NitrogenPosition; nitrogen.IsPositionFixed = true; var carbonAlpha = aminoAcid.GetAtomFromName("CA"); carbonAlpha.Position = approximatedAminoAcid.CarbonAlphaPosition; carbonAlpha.IsPositionFixed = true; var carbon = aminoAcid.GetAtomFromName("C"); carbon.Position = approximatedAminoAcid.CarbonPosition; carbon.IsPositionFixed = true; aminoAcid.Molecule.PositionAtoms(); aminoAcids.Add(aminoAcid); } var peptide = PeptideBuilder.PeptideFromAminoAcids(aminoAcids); peptide.Molecule.PositionAtoms(); return(peptide); }
public static Peptide PeptideFromSequence(AminoAcidSequence aminoAcidNameSequence, PeptideBuilderOptions options = null) { if (options == null) { options = new PeptideBuilderOptions(); } if (options.BuildMolecule) { var aminoAcidReferences = aminoAcidNameSequence .Select(sequenceItem => AminoAcidLibrary.Get(sequenceItem.AminoAcidName, sequenceItem.ResidueNumber)); return(PeptideFromAminoAcids(aminoAcidReferences)); } else { var aminoAcidReferences = aminoAcidNameSequence .Select((aa, idx) => new AminoAcidReference(aa.AminoAcidName, aa.ResidueNumber, null, new List <uint>(), 0, 0)) .ToList(); return(new Peptide(new MoleculeReference(new Molecule()), aminoAcidReferences)); } }
public static Peptide PeptideFromSequence( IEnumerable <AminoAcidName> aminoAcidNameSequence, PeptideBuilderOptions options = null) { if (options == null) { options = new PeptideBuilderOptions(); } if (options.BuildMolecule) { var aminoAcidReferences = aminoAcidNameSequence .Select((aminoAcidName, idx) => AminoAcidLibrary.Get(aminoAcidName, options.FirstSequenceNumber + idx)); return(PeptideFromAminoAcids(aminoAcidReferences)); } else { var aminoAcidReferences = aminoAcidNameSequence .Select((aa, idx) => new AminoAcidReference(aa, options.FirstSequenceNumber + idx, null, new List <uint>(), 0, 0)) .ToList(); return(new Peptide(new MoleculeReference(new Molecule()), aminoAcidReferences)); } }